If lore is so important (I don't feel it yet that way, but can imagine many do) then I'm pretty sure the bright story writers can fix that. But the way I see it is that lore shouldn't prevent what is an ingame issue for many players to be fixed.

A solution could be for example that every item listed on a faction's AH is also listed on the neutral AH, but with a 15% increased cost for the buyer, so the seller isn't affected. Even more, the seller could have the choice to list it there or not (nothing changes for him, he would take the same cut, he just increases his possible buyers). This is just a random idea, I'm pretty sure that a better solution can be worked out. Lore workaround could be that the goblins made a deal with both factions (my imagination & lore knowledge is crap).

Not claiming that I've checked each realms AH, but the ones I did look more or less the same to what I described in the OP. Now the situation is such that if a horde player wants to level alchemy besides JC, he often can't buy the mats off the AH to proceed, whereas an alliance can easily do it. So he has to level herbalism and gather the stuff himself, then delete it and go JC. I don't think that this is a good thing in times where everything gets easier/more accessible to the player. Determined by the faction you chose upon creating an account, and no info that helps you decide.